Fixing deviant vertices after Remesh modfier
Looking at your .blend file, it appears that your mesh doesn't exactly line up for mirroring. This is partially causing the SubSurf modifier to pinch the mesh. To fix this, select the edge loop on the plane of reflection:

Enable Clipping on the Mirror Modifier:

Scale the edge loop on the X axis by 0 (S , X, 0, Enter). Now, as long as clipping is on, the vertices won't deviate from that midline.
Re-enabling the SubSurf modifier reveals that we don't have any pinching any more:

As far as the topology for your window goes, the Remesh modifier is not the best option for you. It has no regard to symmetry and is best used on complex, triangulated meshes, such as Dyntopo sculpts or 3D capture imports. It would be best to just manually retopologize by merging the tris into an n-gon, then cutting it into quads with the Knife tool (K), like this:

This mesh is still symmetrical and preserves your original mesh, unlike the Remesh result. This will also subdivide nicely:

With more subdivisions and smooth shading:


Download the .blend file here: